﻿#region Copyright information
// 
// Copyright © 2012-2013 Yongkee Cho. All rights reserved.
// 
// This code is a part of the SubnetworkToolkit and governed under the terms of the
// GNU Lesser General  Public License (LGPL) version 2.1 which accompanies this distribution.
// For more information on the LGPL, please visit http://bol.codeplex.com/license.
// 
// - Filename: Options.cs
// - Author: Yongkee Cho
// - Email: yongkeecho@outlook.com
// - Date Created: 2013-01-30 2:55 PM
// - Last Modified: 2013-01-30 3:21 PM
// 
#endregion
using System.Text;
using CommandLine;

namespace SubnetworkToolkit.EnrichmentTest
{
    public class Options
    {
        [Option("s", "sourceFile", HelpText = "Specify a source GMT file.")]
        public string SourceFile { get; set; }

        [Option("t", "targetFile", HelpText = "Specify a target GMT file.")]
        public string TargetFile { get; set; }

        [Option("p", "pValueCutoff", HelpText = "[Symbol to Id (0) | Id to Symbol (1)]")]
        public double PValueCutoff { get; set; }

        [HelpOption(HelpText = "Dispaly this help screen.")]
        public string GetUsage()
        {
            var help = new StringBuilder();
            help.AppendLine("Usage : annotation [OPTION]");
            help.AppendLine("Options:");
            help.AppendLine("    -s           source file");
            help.AppendLine("    -t           target file");
            help.AppendLine("    -p           p value cutoff");
            help.AppendLine();
            help.AppendLine("e.g. enrichment -s source.gmt -t target.gmt -p 0.001");
            return help.ToString();
        }
    }
}
